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Changing PileupElement's isSoftClipped to isNextToSoftClip since soft clipped bases aren't actually added to pileups, oops. Removing the intrinsic clustered variants filter from the HaplotypeCaller

This commit is contained in:
Ryan Poplin 2012-01-31 16:06:14 -05:00
parent f9162ea705
commit febc634557
6 changed files with 13 additions and 13 deletions
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4
public/java/src/org/broadinstitute/sting/gatk/iterators/LocusIteratorByState.java
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@ -472,13 +472,13 @@ public class LocusIteratorByState extends LocusIterator {
if (op == CigarOperator.D) { if (op == CigarOperator.D) {
if (readInfo.includeReadsWithDeletionAtLoci()) { // only add deletions to the pileup if we are authorized to do so if (readInfo.includeReadsWithDeletionAtLoci()) { // only add deletions to the pileup if we are authorized to do so
int leftAlignedStart = (eventStartOffset < 0) ? readOffset : eventStartOffset; int leftAlignedStart = (eventStartOffset < 0) ? readOffset : eventStartOffset;
pile.add(new PileupElement(read, leftAlignedStart, true, nextOp == CigarOperator.I, false)); pile.add(new PileupElement(read, leftAlignedStart, true, nextOp == CigarOperator.I, nextOp == CigarOperator.S || (state.getGenomeOffset() == 0 && read.getSoftStart() != read.getAlignmentStart())));
size++; size++;
nDeletions++; nDeletions++;
} }
} else { } else {
if (!filterBaseInRead(read, location.getStart())) { if (!filterBaseInRead(read, location.getStart())) {
pile.add(new PileupElement(read, readOffset, false, nextOp == CigarOperator.I, op == CigarOperator.S)); pile.add(new PileupElement(read, readOffset, false, nextOp == CigarOperator.I, nextOp == CigarOperator.S || (state.getGenomeOffset() == 0 && read.getSoftStart() != read.getAlignmentStart())));
size++; size++;
} }
} }

2
public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/SNPGenotypeLikelihoodsCalculationModel.java
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@ -212,7 +212,7 @@ public class SNPGenotypeLikelihoodsCalculationModel extends GenotypeLikelihoodsC
public class BAQedPileupElement extends PileupElement { public class BAQedPileupElement extends PileupElement {
public BAQedPileupElement( final PileupElement PE ) { public BAQedPileupElement( final PileupElement PE ) {
super(PE.getRead(), PE.getOffset(), PE.isDeletion(), PE.isBeforeInsertion(), PE.isSoftClipped()); super(PE.getRead(), PE.getOffset(), PE.isDeletion(), PE.isBeforeInsertion(), PE.isNextToSoftClip());
} }
@Override @Override

2
public/java/src/org/broadinstitute/sting/utils/pileup/AbstractReadBackedPileup.java
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@ -204,7 +204,7 @@ public abstract class AbstractReadBackedPileup<RBP extends AbstractReadBackedPil
protected abstract AbstractReadBackedPileup<RBP, PE> createNewPileup(GenomeLoc loc, PileupElementTracker<PE> pileupElementTracker); protected abstract AbstractReadBackedPileup<RBP, PE> createNewPileup(GenomeLoc loc, PileupElementTracker<PE> pileupElementTracker);
protected abstract PE createNewPileupElement(GATKSAMRecord read, int offset, boolean isDeletion, boolean isBeforeInsertion, boolean isSoftClipped); protected abstract PE createNewPileupElement(GATKSAMRecord read, int offset, boolean isDeletion, boolean isBeforeInsertion, boolean isNextToSoftClip);
// -------------------------------------------------------- // --------------------------------------------------------
// //

12
public/java/src/org/broadinstitute/sting/utils/pileup/PileupElement.java
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@ -24,7 +24,7 @@ public class PileupElement implements Comparable<PileupElement> {
protected final int offset; protected final int offset;
protected final boolean isDeletion; protected final boolean isDeletion;
protected final boolean isBeforeInsertion; protected final boolean isBeforeInsertion;
protected final boolean isSoftClipped; protected final boolean isNextToSoftClip;
/** /**
@ -34,13 +34,13 @@ public class PileupElement implements Comparable<PileupElement> {
* @param offset the position in the read for this base. All deletions must be left aligned! (-1 is only allowed for reads starting with insertions) * @param offset the position in the read for this base. All deletions must be left aligned! (-1 is only allowed for reads starting with insertions)
* @param isDeletion whether or not this base is a deletion * @param isDeletion whether or not this base is a deletion
* @param isBeforeInsertion whether or not this base is before an insertion * @param isBeforeInsertion whether or not this base is before an insertion
* @param isSoftClipped whether or not this base was softclipped * @param isNextToSoftClip whether or not this base is next to a soft clipped base
*/ */
@Requires({ @Requires({
"read != null", "read != null",
"offset >= -1", "offset >= -1",
"offset <= read.getReadLength()"}) "offset <= read.getReadLength()"})
public PileupElement(final GATKSAMRecord read, final int offset, final boolean isDeletion, final boolean isBeforeInsertion, final boolean isSoftClipped) { public PileupElement(final GATKSAMRecord read, final int offset, final boolean isDeletion, final boolean isBeforeInsertion, final boolean isNextToSoftClip) {
if (offset < 0 && isDeletion) if (offset < 0 && isDeletion)
throw new ReviewedStingException("Pileup Element cannot create a deletion with a negative offset"); throw new ReviewedStingException("Pileup Element cannot create a deletion with a negative offset");
@ -48,7 +48,7 @@ public class PileupElement implements Comparable<PileupElement> {
this.offset = offset; this.offset = offset;
this.isDeletion = isDeletion; this.isDeletion = isDeletion;
this.isBeforeInsertion = isBeforeInsertion; this.isBeforeInsertion = isBeforeInsertion;
this.isSoftClipped = isSoftClipped; this.isNextToSoftClip = isNextToSoftClip;
} }
public boolean isDeletion() { public boolean isDeletion() {
@ -59,8 +59,8 @@ public class PileupElement implements Comparable<PileupElement> {
return isBeforeInsertion; return isBeforeInsertion;
} }
public boolean isSoftClipped() { public boolean isNextToSoftClip() {
return isSoftClipped; return isNextToSoftClip;
} }
public boolean isInsertionAtBeginningOfRead() { public boolean isInsertionAtBeginningOfRead() {

2
public/java/src/org/broadinstitute/sting/utils/pileup/ReadBackedExtendedEventPileupImpl.java
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@ -96,7 +96,7 @@ public class ReadBackedExtendedEventPileupImpl extends AbstractReadBackedPileup<
} }
@Override @Override
protected ExtendedEventPileupElement createNewPileupElement(GATKSAMRecord read, int offset, boolean isDeletion, boolean isBeforeInsertion, boolean isSoftClipped) { protected ExtendedEventPileupElement createNewPileupElement(GATKSAMRecord read, int offset, boolean isDeletion, boolean isBeforeInsertion, boolean isNextToSoftClip) {
throw new UnsupportedOperationException("Not enough information provided to create a new pileup element"); throw new UnsupportedOperationException("Not enough information provided to create a new pileup element");
} }

4
public/java/src/org/broadinstitute/sting/utils/pileup/ReadBackedPileupImpl.java
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@ -71,7 +71,7 @@ public class ReadBackedPileupImpl extends AbstractReadBackedPileup<ReadBackedPil
} }
@Override @Override
protected PileupElement createNewPileupElement(GATKSAMRecord read, int offset, boolean isDeletion, boolean isBeforeInsertion, boolean isSoftClipped) { protected PileupElement createNewPileupElement(GATKSAMRecord read, int offset, boolean isDeletion, boolean isBeforeInsertion, boolean isNextToSoftClip) {
return new PileupElement(read, offset, isDeletion, isBeforeInsertion, isSoftClipped); return new PileupElement(read, offset, isDeletion, isBeforeInsertion, isNextToSoftClip);
} }
} }